Stuxnet's Secret Twin
This new Stuxnet variant was almost entirely different from the old one. For one thing, it was much simpler and much less stealthy than its predecessor. It also attacked a completely different component of the Natanz facility: the centrifuge drive system that controls rotor speeds.
This new Stuxnet spread differently too. The malware's earlier version had to be physically installed on a victim machine, most likely a portable engineering system, or it had to be passed on a USB drive carrying an infected configuration file for Siemens controllers. In other words, it needed to be disseminated deliberately by an agent of the attackers.
The new version self-replicated, spreading within trusted networks and via USB drive to all sorts of computers, not just to those that had the Siemens configuration software for controllers installed. This suggests that the attackers had lost the capability to transport the malware to its destination by directly infecting the systems of authorized personnel, or that the centrifuge drive system was installed and configured by other parties to which direct access was not possible.
What's more, Stuxnet suddenly became equipped with an array of previously undiscovered weaknesses in Microsoft Windows software -- so-called "zero day" flaws that can fetch hundreds of thousands of dollars on the open market. The new Stuxnet also came equipped with stolen digital certificates, which allowed the malicious software to pose as legitimate driver software and thus not be rejected by newer versions of the Windows operating system.
http://www.foreignpolicy.com/articles/2013/11/19/stuxnets_secret_twin_iran_nukes_cyber_attack?page=0,1